Newcastle disease virus (NDV) is an infectious virus in domestic chickens and is endemic in many countries. It has caused huge economic losses worldwide, especially in developing countries where the chickens and eggs are a primary source of economic income and family nutrition for the rural poor. Due to continuous evolution of NDV and unreliable vaccine production and distribution in developing countries, vaccine cannot prevent recurrent outbreaks of Newcastle disease. Therefore, breeding for NDV resistant chickens is a sustainable approach for alleviating rural poverty and food insecurity.

To identify critical genes regulating NDV resistance, an RNA-seq approach was undertaken with spleen tissues from two inbred chicken lines with differing resistance to NDV – Fayoumi and Leghorn. Each chicken line was divided into two groups at hatch. One group was challenged with a lentogenic NDV strain at 21 days post-hatch, and the other was kept in normal condition as control group. Tissues were collected at 23 days (2dpi) and 27 days post-hatch (6dpi) in each group.

For comparisons between challenged and control groups within each line at each time point (n=4/group/time point), at significant level of False Discovery Rate<0.1, 121 and 49 differentially expressed (DE) genes were identified in Leghorn chickens respectively at 2dpi and 6dpi, but only 26 DE genes were identified in Fayoumi chicken at 2dpi, and no DE genes at 6dpi. Seven DE genes encoding interferon-induced and antiviral products, Mx, DDX60, IFIT5, ZNFX1, CMPK2, OASL and USP18, were upregulated in challenged chickens compared to control group in Leghorn 2dpi, Leghorn 6dpi and Fayoumi 2dpi groups. For challenged vs. control at 2dpi, Ingenuity Pathway Analysis predicted inhibitory effect on viral replication and infection in NDV challenged birds of both chicken lines, but stimulating effect on antiviral and immune response in only NDV challenged leghorn chickens.

The identified DE genes and pathways in this study provide a potential way to unravel mechanisms underlying differential resistance to NDV in the two chicken lines and a potential target for breeding of NDV resistant chickens.